Incubator
by Titan5
Summary: John is captured by aliens and experimented on. This is a creepy one.
1. Chapter 1

**Disclaimer: **I don't own Stargate Atlantis or any of its characters, I just borrow them from time to time for fun.

**Warning: **This one is dark and creepy.

**Incubator – Part One**

By Titan5

John Sheppard slid his sunglasses on as he stepped out into the bright afternoon sun. Hearing Rodney mutter about paranoid Ancient scientists behind him, he smiled. They were investigating the ruins of what appeared to be an Ancient outpost and lab, but it was very old and in very bad condition. Every bit of information gleaned so far had been pulled kicking and screaming from the crumbling database.

"Colonel Sheppard!" Three men from the local town were coming down the path. Teran, a man in his mid-thirties with long brown hair and beard to match, led the group. He was smiling and waving. The two men following him were younger, best friends in their early twenties. Sren had shoulder length blonde hair with blue eyes and baby face. Harndt had dark hair cropped short, with a constant five o'clock shadow and a crooked nose. Both men were about Sheppard's height and build, lean and wiry.

John gave a short wave as he stepped out of the doorway and into the full sunlight. He gave a nod to Teyla and Ronon, standing on either side of the entrance as he went forward to meet the men. The two members of his team came up behind him as he and the men from town came face to face.

Teran smiled at them in greeting. "Colonel, Teyla, Ronon. We have come to share some news with you. Two boys returned from their hunting trip to tell of some strange beings near the edge of the Calahoun Meadow. We are going to investigate and since it is not far from here, we thought you might like to come."

John quirked one corner of his mouth up and looked at the sun's placement in the sky. "How far is not far, because we told our people we'd be back in a few hours?"

"Shouldn't take more than two clicks of the sun from here," said Harndt.

John looked at Teyla, who smiled at him. "About thirty minutes."

John nodded, flashing a lopsided grin at Teyla for the translation. "Okay, things are pretty quiet here."

"Perhaps I should come as well," offered Teyla.

John looked back at the temple and then at Teyla. He didn't expect any trouble. They had negotiated a trade agreement with the Baradians three days ago and during the celebration that followed, they had told the Lanteans about the ruins. The team had come back the last two days to examine the place with the blessing of the town. Teran had told him that their scientists hadn't been able to learn anything from it, leaving the Lanteans to use or take whatever they wanted. Rodney had managed to get part of the place to run in spurts, during which he worked frantically to extract whatever information he could. That left John, Ronon, and Teyla to stand watch and try not to be bored out of their minds. John welcomed the distraction.

"Okay, I doubt Rodney needs all of us here to stand guard. I'll let him know where we're going and that Ronon will still be here."

Ronon frowned at John. "Why should I have to stay here?"

John gave him an easy smile. "Because she asked to go first. Sorry buddy, but I need someone here to keep Rodney out of trouble." John heard Ronon growl behind him as he sauntered over to the doorway and peered in. "Rodney, Teyla and I are going with Teran to check out some strangers. Ronon's out here if you need anything."

Rodney never looked up from his place on the floor as he worked on one of the consoles. "Yes, yes, checking out strangers, whatever. Just go away and quit bothering me. Why is this connected like this? I thought these people were supposed to be technologically advanced."

John chuckled as he joined the others outside. "Okay, let's go."

Teran laughed and smacked John on the shoulder. "I knew you would want to come with us. You are a curious sort, as I am." He began walking past the ruins, with John and Teyla walking beside him. Harndt and Sren continued to follow behind.

"So, what do you know about these strangers?" asked John.

"The boys claim there were four of them and that they were very tall and slender with white skin and white robes. We have never encountered such people before."

"Doesn't sound familiar." John glanced at Teyla. "Have you or your people ever seen anyone like that?"

Teyla shook her head. "No, I do not believe so. I do not recall hearing of anyone like them in our travels either."

"Let's just hope they aren't kin to the Wraith," said John wryly.

They talked and kidded with a friendly banter for the next half hour. John liked these people. Their technology level was similar to early thirties or forties on Earth, except for transportation. They still relied on horse-like animals and walking to get places, but they never had very far to go, so that worked for them. They were open and friendly, reminding him of the Athosians in many ways.

"We are here, Colonel Sheppard. The meadow is just ahead," said Sren, pointing to where the trees opened in front of them. They cautiously and quietly walked up to the edge of the trees and stood, gazing across the tall grass.

"Look, there," whispered Teyla, pointing almost directly across the field. Four tall figures stood wearing white robes.

John looked at Teran. "Anyone you know?"

"No," Teran whispered back. "What should we do?"

John studied them. He couldn't tell what sex they were, they all looked alike. They were easily Ronon's height, with hoods that covered their heads and part of their face. He could see that their skin was milky white, their eyes large and dark, but they appeared humanoid. "They don't seem to be armed. I guess we see what they want." He led the way into the field, his arms raised. "Hi, we mean you no harm." He could hear the others coming along behind him. The robed figures made no move to come their way, just standing near the edge of the trees.

The group walked slowly across the field until they were in the middle. John paused, staring at the strange figures in front of them. "My name is Lt. Colonel John Sheppard. We just wanted to talk to you, see if we could help you or anything. Could you tell us who you are or where you're from?" The others had come up beside him so that they stood in a straight line, watching the strange white creatures.

One of the figures stepped out from the others a few feet and stopped. He reached into the pocket of his robe and pulled out a metal disc. Holding it up as if showing it to the group in the meadow, he gave a short nod and twisted his wrist. The last thing John saw was a blue light burst forth from the disc.

oOo

Rodney cursed under his breath when he banged his head on the bottom edge of the console as he was trying to crawl out from underneath it. Glancing down at his watch, he sighed. He'd wasted three hours trying to get this piece of junk working. Just as he'd be about to bring information up, it would begin to flicker and then go out completely. All he had to show for his efforts were scraped hands and a crick in his neck. And a bump on his head, which he now rubbed.

Rodney got to his feet and stretched, taking a long look at the room. "I'm done here," he admitted out loud to himself. "Stupid Ancients," he muttered as he made his way stiffly to the doorway and squinted in the afternoon sun. It took a moment for his eyes to adjust where he could see anything besides painful glare. He finally made out Ronon standing in front of the ruins, looking down what could have been a poorly maintained path. Looking around, he noticed Sheppard and Teyla were not there.

"They not back yet?" he asked, trying to remember if Sheppard had mentioned how long they'd be gone.

"No, and they should have been. They aren't answering their radios either."

Crap, what had Sheppard gotten himself into this time. "What should we do? Can you track them?"

Ronon nodded. "Yeah, they left a pretty obvious trail. You wait here."

Rodney shook his head. "Oh, no, I'm coming with you. Colonel Calamity is probably in some kind of trouble and you might need me."

Ronon scowled at the scientist. "You know what he said he was doing to you the next time you called him that."

Rodney shrugged in feigned nonchalance. "Well, he's not here, is he?" Ronon gave him a tight grin that made him shudder. Tattletale. "Anyway, I'm going."

Ronon shook his head. "No. If they are hurt, we'll need to contact Atlantis for help. If you stay here, I can radio you and you'll be closer to the gate."

Rodney had to admit, the plan made sense. "How long have they been gone?"

"Over two hours and Teran said the meadow was only a thirty minute walk. Something is wrong."

Rodney felt cold fear tie his gut into a big, painful ball. "Maybe I should go ahead and start walking to the gate. I could be almost there by the time you reach the meadow so I could call for help that much faster."

Ronon nodded once. "Sheppard always says you're the genius."

Rodney perked up, his eyes going wide. "Really, he says that?"

Ronon held onto his stoic expression. "No."

"Oh." Rodney tried not to look disappointed. "We'd better go."

"Yeah. Be careful, McKay. Sheppard will kill me if I let anything happen to you." Ronon's mouth twitched into a small smile.

"You too, big guy. Find them."

"I will." Ronon turned and followed the makeshift path that led away from the ruins and the gate. Rodney hurried back into the ruins and gathered his stuff into his pack. He was afraid for his friends, but he felt good about what Ronon had said. He smiled. He knew Sheppard probably really had admitted he was a genius to Ronon and that he would be angry if anything ever did happen to him. Friendship had its annoying little problems, but all in all, he was glad he finally had a few friends. He grabbed his now full pack and headed for the gate.

Twenty minutes later, he could just see the gate rising up in the distance. Several people from the town were walking toward him and he was grateful for the opportunity to tell them what had happened without losing time by actually going into the town.

"McKay? You there?"

Rodney came to abrupt stop and tapped his radio. "I'm here. Did you find them?"

"Teyla is unconscious, but there is no sign of injury. I think she may have been stunned by something. Sheppard and the others are gone. They were here and the grass is beaten down as if they were all stunned here in the middle of the field. But the others are just . . . gone."

"Can you tell where they went? If they were dragged or if they walked?"

"There are no tracks leading away. They are just . . . gone."

Rodney's stomach dropped like a rock. "That means they had a ship and probably beaming technology. We have no way to follow them." He sighed, fighting the powerbar from earlier that was trying to make a reappearance. "I'm almost to the gate. I'll let Atlantis know and get a jumper and med team here for Teyla."

"You should let the people from town know."

Rodney watched the group of men and teenagers drawing near. "I will. There's a group here near the gate. Take care of Teyla."

"McKay, we'll find him."

Rodney kicked the dirt, sending it spraying out in front of him. "Yeah," he said noncommittally. _And the Wraith are going to surrender this year because they are so afraid of us, _he thought bitterly.

oOo

Consciousness came back slowly, little snippets at a time. John could hear sounds of movement and an occasional metal clinking, but it took several minutes before they began to register. Next he became aware of an antiseptic smell, and he relaxed. Infirmary. The relaxed feeling didn't last long, because he began to realize something was wrong. He wasn't lying on a soft bed, he was lying on a cold, metal surface and he was pretty sure he had no clothes on. He shivered, as much in fear as from the chill.

He was in restraints. His hands and ankles were bound to the table with no slack whatsoever. They weren't tight enough to be painful, but they eliminated all movement. As he struggled to open his eyes, his heart beginning to double time in his chest, he also realized there was a strap across his forehead, holding his head still, and another across his chest. If you could die from fear, he was well on his way.

He looked up to see two of the white creatures from the meadow standing on either side of him. They still wore white, but now they had on what appeared to lab coats. Since no hoods were involved this time, he cold see their elongated faces, with tiny mouths and two small slits where he would have expected a nose. Their eyes were large and dark, with no sign of a pupil and their foreheads were twice as long as he expected. They had no hair, just a lobed head with blue veins running close to the surface.

John flinched when one set of cold hands pressed his hips down firmly on the table and another set began to handle his groin. Fear rocketed through him, its level upped by the fact that he couldn't see who was handling him down there. "Please . . . don't," he pleaded.

One of the figures beside him put a hand with long fingers on his shoulder and stroked his cheek with the other hand, almost as if trying to comfort him. He sucked in a quick breath and held it at the discomfort of feeling a tube being inserted into his urethra. They were putting in a catheter. He didn't know whether to be relieved or more afraid. Why would they be doing that? When they finished and released him, he let out the breath, shivering violently. One of them covered him from the waist down with a sheet or something similar. Terrified didn't even begin to cover how he felt.

He shifted his eyes since he couldn't move his head, trying to see more of the room. It looked like a cross between a medical facility and a lab and that scared the crap out of him. He discovered a large bag of fluid hanging from a pole, connected to his right arm by a tube. But he got the feeling it was a little more involved than a simple IV. The tube disappeared into an area covered by bandages on his forearm and he was now aware of a stinging sensation just about where it seemed to enter. The bag and tube were both larger than anything he'd seen in the infirmary. A similar sensation in his other arm caused him to shift his eyes to the other side to see a mirror image of the set up. They were pumping large amounts of something into him. His heart was beating so hard now that he was dizzy and felt like he could barely breathe. At least the times he'd been tortured, he'd known what to expect and why there were doing things to him. This was different.

Three of the creatures drew into a huddle, looking at one another, but not speaking. One of them pointed to a screen turned away from him and then they all looked his direction. He became aware of pads on his chest and wondered if it was some kind of heart monitor. Maybe they had noticed he was on the verge of giving himself a heart attack. At this point, he thought maybe he would welcome it, because he was pretty sure he wouldn't enjoy whatever they had planned for him. He'd also noticed a tray of instruments next to the table he was tied to and he figured they were for him.

The group broke up and one of them began to stroke his face gently before placing its fingers on his temples and pressing firmly. He suddenly felt dizzy and like he was falling. The world darkened around him and a voice began talking in his head.

"Do not be afraid. We will try to make this as painless as possible. Struggling will only make it more difficult for you. I am sorry for what we must do, but it is necessary for our survival."

John projected his thoughts, hoping the being could hear him. "What are you going to do? Look, maybe we could talk about this. Maybe there's another way and my people could help you. You don't need to do this. Please, we didn't intend any harm to you."

"We know you did not intend harm, and that is why we will strive to make this as easy on you as we can. I'm afraid there will still be pain involved, but we will try to minimize it when possible. We are sorry for your suffering, but as I said, it is necessary."

Instead of diminishing, John's fear only began to escalate. "What about the others?"

"We took the four of you that were male. We cannot use females, so the one that was with you was left where the others can find her. She will be fine when she awakens."

John was relieved to find that Teyla wasn't here, about to be experimented on or operated on or whatever they were planning to do. He wished the others hadn't been captured with him. That meant four of them would suffer and he had no way to help any of them.

"Where are we?"

"You do not need to know. But you must try to relax and let us do our work. I'm afraid there is nothing you can do to change your fate. You should accept it and it will be easier on you. I must go now. We are about ready to begin."

"Wait, one more question. Will we survive?"

The hesitation said more than the words. "We have not perfected the method yet. We will work to keep you alive so that you may return to your world when we are finished, but we have not had any success in that yet. I'm afraid you should not expect it."

With that announcement, the connection to the white alien was gone. He blinked his eyes a few times at opening them and looked around with his limited field of view. Two of the creatures had some type of machine poised over his stomach and they were staring at a monitor screen. A third one came up on the other side and began pushing against his abdomen, moving his hands around until he found what appeared to be the right spot. One of the aliens at the monitor gave a short nod and then something tickled his stomach, almost like someone writing on it.

And then the action began. They all pulled masks up over their faces and began to put on gloves. One of them began washing his stomach with a cool cloth and another approached him with a cylindrical apparatus about eight inches long and one inch in diameter. A clear tube with liquid was loaded in the back and the alien pressed it against the side of John's neck. He heard a small hiss about the same time as he felt a sting. Great, more drugs. Almost instantly, the feeling in his limbs began to fade. He could see them touching his stomach still, but his ability to feel their gloved fingers slowly faded away. The feeling crept up his chest until he realized he was having trouble breathing. Was that supposed to happen?

He was about to panic. He wanted to shout that he could no longer breathe as the pain built in his chest, but his face was numb and he couldn't talk. His vision was starting to gray and black spots began dancing around when the strap on his forehead was lifted and an alien tilted his head back. He could see the tube in its hand and he knew what they were about to do. He'd been intubated before, but never when he was conscious. He tried to close his eyes, but his eyelids wouldn't work. Oh crap.

He was surprised when he couldn't feel anything. He didn't feel the guide they put in his mouth or the tube that slid down his throat. There was no gag reflex, because it was like he was watching it happen to someone else. Whatever they had given him was good. His head was straightened back up and the tube connected to something that began to pump oxygen in him, relieving the burn in his chest and making the spots go away. He could see the strap being replaced in his peripheral vision. He wanted to laugh. He couldn't feel or move any part of his body. Did they really think he was going to get up and run off at this point?

All he could do was lie and look at the ceiling. The only sound was an occasional clink of an instrument or a sucking sound. He couldn't even shift his eyes down to see what they were doing. Ever once in a while he got a glimpse of a bloody glove or instrument being put back on the tray. Whatever they had given him had slowed his heart considerably. He might be afraid the drug would stop his heart, but that actually seemed like the lesser of two evils. He was probably going to die anyway. His body might not be working, but his mind was. He had already figured out they probably were not on the planet and that meant his team had no way to track him. Escape from this place looked doubtful, although he wouldn't stop trying to find a way. Realistically, he probably wasn't walking away from this one. He'd have to be satisfied with the knowledge that the rest of the team was safe.

At some point he became aware that he was starting to feel pressure and a little tugging from his stomach. There was also a slight sensation of the tube in his throat. He blinked, and realized he could shift his eyes. He moved them to look down as far as he could. One of the aliens held out a jar and something was removed from it and disappeared from his field of view toward his stomach, where they were working. The jar was set aside, empty. The fear that had been somewhat muted by the drugs began flaring up again. They were putting something in him. Images of the movie _Alien_ suddenly flashed in his head, to be replaced with images of monsters bursting forth from his stomach. He began to wish he had given himself a heart attack. It seemed like a much better way to die.

Sensation was beginning to come back quickly. He could now tell they were closing him up. The pressure was just at the point of evolving to pain when they seemed to finish. He was both relieved and scared, because the tube in his throat was now beginning to choke him. He tried to relax and let the machine breathe for him, but he still found himself beginning to gag.

Movement to his side caught his attention and he shifted his eyes, hoping they had noticed and would remove the tube now. Instead, the alien was replacing the now empty bag of fluid on his right with another bag, this time of a blue-tinted liquid. John watched the blue line snake down the tubing and disappear under the bandages. He knew the instant it hit his vein because that's when the fire began. It spread up his arm and across his shoulder, down into this chest. From there, it exploded up his neck to his head and down through his torso. All conscious thought was relinquished as the pain took over. He had no idea how long it lasted, but it was all there was for what seemed like an eternity. Eventually it began to fade and he gratefully allowed the darkness to move in.

oOo

Elizabeth followed Carson back to Teyla's bed. The Athosian was propped up with pillows, her expression still somewhat dazed. She noted that Carson had started an IV and had her on a heart monitor. He'd told her the stun had been far more severe than anything they had encountered so far, but she was still surprised at the apparent severity and the caution it had inspired.

"Teyla, how are you feeling?"

Teyla's eyes were a bit glassy, her lids only half open. "I am fine. What about Colonel Sheppard and the others?"

Elizabeth shook her head. "Nothing yet. Ronon and Rodney took two jumpers back to search. Can you tell me what happened?"

Teyla gave a small nod and recounted what had happened. "The blue light is the last thing I remember. I do not even recall falling. When I woke, I was here in Atlantis."

"You were out for several hours," said Carson. "It seems to be a much stronger stun that what the Wraith have."

"I did not feel the pins and needles upon waking."

Carson nodded. "Aye, it seems to work a bit differently on the nervous system. I think it-"

They were distracted by the sounds of several people coming through the door of the infirmary. Rodney, Ronon, Lorne, and Nick all entered the room, their expressions downcast. Nick Straughn, Carson's second in the infirmary, set the medical bag he was carrying down near a set of shelves and then followed the others to Teyla's bed.

"Well?" asked Elizabeth. "Anything?"

Rodney shook his head and looked down at the ground for a second. "Nothing. Ronon and some of the people from town searched all the way around the meadow, but found no sign of tracks or anything. Lorne and I took the jumper up into space around the planet, but found nothing there as well. I'm pretty sure they had a ship in orbit, beamed down and grabbed Sheppard and the others, and then beamed back up. They're long gone by now and we have no way of tracking them."

"There has to be something you can do," pleaded Teyla, sitting up straighter in the bed.

"There isn't," said Rodney. "He's just . . . gone."

Teyla's face darkened. "Then he will escape and find his way back to Atlantis. He is not gone."

Rodney's face reddened. "I didn't mean gone as in gone for good or dead. I just meant that he seemed to have disappeared. Of course, he'll turn up. He always does."

Nick frowned and looked at Rodney. "Is there _anything_ we can do to try to find him?"

Rodney furrowed his brow for a second and then snapped his fingers. "Maybe. If Radek could give me a hand. Maybe we could put together something to look for traces of the ship while it was in orbit. Depending on their power source, sometimes trace amounts of exhaust elements or ionized particles are left behind. With the right kind of sensors, maybe we can detect a trail of some kind."

Elizabeth looked relieved that there was at least something they could try. "Do it and take whoever or whatever you need."

Rodney nodded. "We'll have to hurry. If there is a trail, it won't last long." He rushed out of the infirmary, mumbling to himself about what he needed to do.

Elizabeth patted Teyla on the arm. "At least it's a chance."

oOo

John awoke to a combination of more freedom of movement and more pain. His wrists and ankles were still restrained, but with a small degree of movement allowed. There was no longer a strap on his head or chest and he was glad to be on a soft bed instead of a metal table. As soon as he opened his eyes, the room began to spin and he felt nausea roll through his stomach. He began to gag almost immediately. Two of the aliens appeared by his side. One of them opened his mouth to shove something soft and flat, about the size of a squished marshmallow inside and then proceeded to hold his jaw closed. He automatically struggled against it, feeling like he was going to choke, but he was incredibly weak and his captors were strong. The second alien held his shoulder pinned to the bed with one hand and pressed against the wound in his stomach with the other. Pain exploded through his gut, making him wonder if circumstances could possibly get any worse.

The pain momentarily overtook the nausea. A few seconds later, he discovered that whatever they had placed in his mouth was melting and as it trickled down his throat, the nausea was receding. He began to relax and as his struggles lessened, so did the grip of the white aliens. When they let go, he opened his mouth and panted. That was when he realized the intubation tube was gone. He drifted for a few moments and when he opened his eyes again, he found the aliens had left him alone.

John took the opportunity to look around. He still had the two huge IV bags, but they were both clear. He hoped he never saw another one of those blue bags again. He lifted his head a little on a shaky neck and then let it drop back to the pillow. His abdomen was bandaged and what appeared to be two tubes with plugs in the end stuck out from the bandages. He didn't even want to know what that was for, although he was sure he'd eventually find out. The catheter was still in place, meaning they probably didn't plan on letting him out of bed for anything. His entire body ached, probably a remnant of the blue fire they had put in his IV.

"Colonel Sheppard?"

John turned his head to his left, surprised that the soft, timid voice had come from Sren, lying in the bed next to him. He seemed to be in the same shape as John. Sheet pulled to his waist, bandaged stomach and forearms, two IV bags. Beyond him he could see Harndt and then Teran. "You guys okay?"

"No, Colonel, we aren't," said Sren, his voice shaking slightly. "They put something in me. They cut me open while I was still awake and put something in me. Why are they doing this? It hurts and they won't give us anything for the pain."

John could sympathize with the man. His gut was on fire and his entire body trembled with a combination of fear, weakness, and pain. He was almost terrified beyond words of what lie ahead for them. But he also knew that panic would not get them anywhere. "I know. It looks like they did the same thing to all of us. Have they told you anything?"

Harndt lifted his head slightly to look at John. "I don't think they can talk. I think they communicate with their thoughts. One of them touched my face and tried to calm me down, but I heard his voice in my head. He just said he was sorry, but this was necessary and we shouldn't fight it."

John nodded. "Yeah, that's pretty much what happened to me." He looked down at his wrists and pulled against the restraints with all his might, but they didn't budge. He tried twisting his wrists in an effort to slide out, but there wasn't enough room to make any progress. All he did was make his wrists hurt along with the rest of him. Exhaustion finally made him go limp, panting to suck in enough air.

"They're too tight," said Teran.

John grimaced and closed his eyes a second before rolling his head to look at the man. "Yeah, I think I figured that out." Looking across at Sren, he could see the bandage on his stomach better than he could see his own. The man also had two small tubes sticking up out of the bandages. "Does anyone know what those tubes are?"

Each man lifted his head to look at his own stomach. "No," said Sren.

Teran looked over the two men in the middle to John. "They did not tell us, but we may be about to see." He nodded past John.

John turned to see two of the aliens enter the room with a tray. Four cylinders similar to the one they had used on his neck lay on the tray. They stopped at John's bed first, since his was the first they came to. One of the aliens removed the plug from the end of the first tube and cleaned the entrance.

"Wait, what are you doing? What is that?" John tried not to sound panicked as he asked the questions, but he was pretty sure he wasn't successful. The two beings ignored him completely as the second one took one of the cylinders. The tube in the back of the device contained a yellowish liquid, which he injected into the tube. The first alien then wiped down the tube again and replaced he plug. They moved to each of the others, performing the same procedure on each man. When they were finished, they left, having never uttered a word. Each man had questioned them, with Sren begging them to stop, but they never gave any indication they heard them. As he watched them leave, John realized they didn't have ears. Maybe they really couldn't hear them.

"We're going to die here, aren't we? And they'll never even know what happened. Ansa will never know I was going to ask her to wed me." Sren closed his eyes and a tear rolled down his cheek.

John lifted his head and leaned toward the other man as much as his bindings and wound would allow. "Look, you can't think like that. We aren't dead yet and things can happen. I know my team is looking for me. And your people will be looking for you, right? We can't give up. An opportunity may present itself. They keep apologizing, like they feel bad about what they are doing. Maybe they'll realize how wrong this is and stop, send us home."

Sren rolled his head over and looked at John. "Thank you for what you are trying to do. I do not believe it will happen . . . but I appreciate that you are trying." He turned his head to look at the ceiling. John shifted back into the bed, battling his own internal demons. It was taking everything he had not to slip into full blown panic and just scream and fight until they knocked him out or killed him. He couldn't lose it. There were three men next to him that didn't deserve to be abandoned just so he could try to end his own pain. _Suck it up, Sheppard. This could be a long one._

oOo

Elizabeth entered the jumper bay and waited for the back hatch to open. Rodney and Radek shuffled out of the ship, their faces full of defeat. "Nothing," said Rodney. "We couldn't find a trace of anything."

"That is not entirely true," said Radek. "We did find a few traces, indicating a ship was there. But there was not enough to make a trail, much less follow."

Rodney snorted. "Like I said, nothing. It's up to him, now. There's no way to track him. I hope he can pull off one of his miracles."

Elizabeth sighed and looked down. "Me too."

oOo

John jerked away from the touch, snapping his eyes open to find two of the alien creatures on either side of him. They stood still for a few moments until he lay back against the pillow. He realized he had dozed off and they had caught him off guard. "What do you want now?" he asked bitterly, not caring if they could hear.

One of them hung a bag of something gray and slimy looking on the pole just below the other bag. He noticed for the first time that the creature had what almost looked like a small scar over one eye. Scar held the tube connecting to the bag until the other one had unplugged and cleaned the port on the second tube, emerging from lower on his stomach. He then connected it. Whatever the gray slime was, it was now on its way to being inside him.

"Okay, that's just nasty. What is that? Do you think you're feeding me, cause that's not what I eat. Could we just talk about this please?" Scar and Shorty (because the second one actually seemed shorter than all the others) checked the connections and his restraints and then left. He noted that they didn't hook the others up to the gray junk. Didn't that make him feel special.

He lay watching the stuff move into him with morbid fascination. What was it and what would it do to him? He tried to keep from tensing up, because that made the incision pull and hurt. He guessed it took almost an hour for the small bag to empty. About the time it was finishing, he felt his lower gut begin to roll and cramp. Scar and Shorty came back to disconnect his little tube and they noticed his discomfort. Scar did the stroking thing with his cheek again while Shorty gathered some things together.

The next thing he knew, they had pulled the sheet off, exposing him to the world. Two other aliens came in and got on either side of him. The new guys slid their hands under his hips and lifted him while Scar and Shorty put something around him. He finally looked down to see what they were doing when someone got hold of his manhood again, shifting it out of the way while being careful of the catheter. He gasped. They were putting what appeared to be a large diaper on him. He quit watching and looked at the ceiling, his face red and hot. He could feel the eyes of the others on him, watching out of curiosity. They finally pulled the sheet back over him just as the cramps got worse.

He saw Scar and Shorty move over to Sren and hang a bag of gray goup on his IV pole. Next. The cramps suddenly began to tear through him like someone ripping him open and eviscerating him. He moaned and twisted, a cold sweat covering his face. He'd have give just about anything to curl up on his side in a ball. Being strapped down made the pain even worse, pressing down and threatening to cut off his breath. It almost felt like the whole area between his navel and his groin was rippling with the waves of agony surging through him. A sudden sharp pain caused him to cry out, followed by a rush of warmness in the diaper.

He lay shivering and wrung out and miserable. His entire body shook uncontrollably and even his torso was covered with sweat. He was unable to move, his muscles devoid of energy. Scar and Shorty had finished with Sren and had been loitering by the edge of the room as if waiting. They now nodded at one another and came over to him. He was pretty sure the clean up was the most humiliating thing he'd ever been through. It seemed to take forever and the others averted their eyes or turned their heads entirely, an action he was grateful for. They took him out of restraints long enough to get him cleaned and dried, undoubtedly realizing how weak he was. When they were finished, they checked the catheter and replaced the sheet, making him sigh in relief.

He watched as Sren began to squirm in pain and the diaper crew came in to get him ready. He closed his eyes and tried not to think about it. This sucked worse than anything he'd ever been through. He almost wished he was back in Afghanistan.

oOo

At the end of what John thought might be a week, they ran another bag of blue liquid through each of them. When they hung the bags, they each begged for them not to, but to no avail. When the drug hit their system, they screamed. John wasn't sure how long it went on. All he knew was pain for what seemed like a very long time before he finally passed out. When he woke up, he was hoarse and thirsty. But they never gave them water. Once or twice a day, they got a small disc to suck on that melted and soothed the throat a little, but never anything by mouth to eat or drink. That made him wonder even more what they had done to them.

The gray slime meal was given once a day, and was always followed by the worse case of cramps John had ever experienced and the humiliating diaper patrol. He was almost used to the clean up afterward. Almost. He at least thought he'd stopped blushing.

Somewhere around ten days into the nightmare, John realized they were going downhill. He'd noticed swelling around his arms and legs and belly. He had even less energy than before and he drifted in and out more often. He didn't fight the alien creatures any more and he'd quit looking for opportunities to escape. The others were sleeping more as well and their words were slurring sometimes. He was pretty sure if they took off the restraints, none of them would be capable of getting off the bed, much less making a run for it. Sren had been right. They were going to die here.

John woke suddenly to a gurgling sound. He twisted his head to the left to see Sren staring wide eyed at him, making the gurgling sound as he tried to talk. Blood bubbled from his mouth and nose. John tried to sit up, a reflex action, before the restraints pulled him back down. Three of the aliens rushed in and surrounded Sren, working over him for several minutes. When they finally backed away, Sren lay still, his glassy eyes staring sightlessly up at the ceiling. Scar bowed his head and then slowly nodded to the other two aliens, who silently wheeled the bed out of the room.

John looked at Harndt and Teran, knowing that his expression probably showed as much fear as theirs did. Teran finally laid his head back on the pillow. "He was a good man."

"We're all going to die, just like he did," said Harndt.

John didn't feel like arguing, like trying to convince them otherwise. "Well, at least then it will be over," he said with resignation. At this point, dying just didn't seem all that bad.

"Good point," Teran said quietly.

oOo

Elizabeth entered the mess hall and went through the line. She wasn't even sure what she gathered on her tray to eat. It didn't seem important any more. She stood looking around the hall for a minute, wishing she could see John at a table, playfully motioning her over. God, she missed him. It was two weeks tomorrow and no sign of what had happened to him. The SGC was already talking about having Caldwell stay as John's replacement when the _Daedalus _arrived next week.

"Elizabeth, over here."

She shook herself out of her stupor to see Rodney motioning at her. Teyla and Ronon were sitting with him. She gave a brief smile and nod and headed over to join them.

"Thank you, I guess I was day dreaming," she explained as she sat down.

"That's okay, we're a little lost ourselves," said Rodney.

"We were just discussing how much we miss John," said Teyla.

Ronon grunted, stabbing his meat with his knife almost like he was attacking it. "There has to be something we can do. I hate sitting here."

Elizabeth nodded. "I know. But we've interviewed all our allies to see if any of them know anything about these beings that took John and the others. No one has ever seen or heard of them. There's no way to track them. I just don't know what else we can do at this point. I'm hoping Colonel Caldwell might have some ideas when he gets here."

Rodney snorted. "Like that's going to happen. He's got Sheppard's position here all tied up. Why would he jeopardize that?"

"Because even though he covets John's command of Atlantis, I don't think he would intentionally do anything to hurt John to get it, including abandoning him when he could help. Steven is ambitious, but he isn't cruel."

Rodney snorted again, showing his disdain for the man. "Maybe."

"Elizabeth," Teyla said softly. "What do we do if John doesn't come home?"

Elizabeth looked down at the table. That was the question she had been carefully avoiding for the past two weeks. "I don't know. I honestly don't know."

oOo

John felt like his eyes were rolling around in his head as he tried to open them. Waking up was becoming increasingly difficult. He felt like an elephant was sitting on his chest and his gut rolled with pain. He didn't even have enough energy to squirm. He stared at the ceiling for a while, wishing he'd just go ahead and die. Working up his nerve, he looked to his left to see Teran still there. Harndt had died last night in much the same way as Sren. He wondered if it would be him or Teran to go next.

Scar came in to check the readings on the monitor. They had hooked him and Teran up to some kind of monitoring system after Harndt died. Shorty moved past him to go check on Teran.

"Why don't you just . . . kill us. . . be easier," he said, gasping for air as he talked. Scar fiddled with something on the tray for a moment and then placed an odd-shaped oxygen mask over his face. John almost laughed, thinking it wouldn't help when blood began bubbling up his throat. Scar looked down at him and then reached out, placing his hands on John's temples. John was immediately surrounded by swirling clouds, making him dizzy.

"John Sheppard, I have much to tell you."

The voice was in his head again. At least now he could tell the creature what he thought. "You've already killed Sren and Harndt. Why don't you just kill us too and get it over with?"

"I must explain what we have done. Why this was necessary. My species is dying. There are only a handful of us left and the last generation was sterile. We had a few embryos frozen from the previous generation, but no way to incubate them. They must go through an early stage in a pouch in the male, but we have evolved to a higher state of intelligence that has also left us almost without gender. We no longer have anyone suitable to carry the embryo. Your form is similar to the form we used to have. We have discovered that the stomach of an adult male is suitable for a short period of development. The acidic environment is suitable and the male hormones are close to what is required. We added the other necessary chemicals to the fluids we were giving you. We had hoped to bring the embryos to a suitable stage of development where we could transfer them to the artificial environment we had prepared."

"So what happened to Sren and Harndt?"

"The embryo produces toxins in ever increasing amounts. That is why we have kept fluids moving through you, in an effort to dilute the poisons so you would survive long enough. But your liver and kidneys are showing signs of stress. You are dying and there is nothing we can do. The embryos are also dying. We have decided to send you home and to give up. We will be the last."

"Maybe our scientists could help. I tried to tell you in the beginning, we help people when we can. None of this was necessary. No one had to die."

"I am sorry about the two deaths. I only hope that you and your companion can be saved. I am ashamed that we have taken our research this far. We should have accepted our fate gracefully. There was a time when we would have done anything to avoid taking a life. I regret that we let our fear cause us to fall so far. And thank for your offer, but after what we have done, we cannot accept your offer. We deserve our fate. Perhaps it is for the best since we have let our values drift away from us."

"What happens now?" John was almost afraid to believe that he was going home. He didn't think he could handle it if he let himself believe, only to find out he'd been tricked.

"We are translating our procedures into data that your people can interpret. Our ability to communicate with you in this way allows us to assimilate your language readily. Your healer will be able to help you better if he understands what was done. We will leave this here with you and contact your people with your location so that they may come and get you."

John didn't bother to tell him that the planet he was taken from was not his home. If they contacted the planet, the Baradians would pass the information on to Atlantis. Maybe this was real. "Okay, what about that stuff you kept putting in us? The stuff that made us so sick and the other stuff?"

"I am sorry for the discomfort. Since your stomach was modified into a pouch for the embyo, we could not allow you to eat. We had to limit what went into your stomach. We made a nutrient mash that was predigested and added a pathway to take it directly to your small intestine, just below where the stomach joins. I'm afraid we could not allow you to get up and down, so we had to manage your waste excretion as well. We have found this method takes a minimum of time and effort to deal with. The other pathway we created went to nourish the embryo in your stomach pouch."

John grimaced, wishing he'd wake up to find this was a nightmare.

"As I have said, we are sorry for the pain and discomfort we have caused you and I truly hope you are able to survive. I must go now. The message is already being sent and your friends should be here shortly to help you."

The connection ended, leaving John dizzy and disoriented for a while. When he opened his eyes again, he and Teran were there alone.

TBC


	2. Chapter 2

**Note: **I am not a medical professional, so this chapter is probably riddled with mistakes that will make those of you who are cringe. I apologize. Just remember, Stargate Atlantis is science _fiction _ and that medicine is a science (in spite of what Rodney says), so I'm giving you a lot of medically inclined science _fiction_. Yeah, I know it's lame, but it was the best I could come up with. Sorry!!

**Incubator - Part Two**

By Titan 5

Elizabeth jumped when the alarm began blaring.

"Unexpected off world activation," said Chuck as Elizabeth came out of her office. "We're getting a transmission from the alpha site."

"Put it through," she said, the excitement from a moment before dissolving.

"_Atlantis, this is Lt. Carlton. The Baradians just contacted us to let us know that they have received a transmission from the people who took Colonel Sheppard and the others. They gave them the address of their location and the Baradians want to know if we want in on the rescue."_

Elizabeth's heart jumped in her throat, making it hard to speak. "Tell them we'll have a jumper there with rescue and medical personnel in a few minutes."

"_Roger that. The Baradians said the message was strange, apologetic even, and that there would be no resistance."_

"Well, we've heard that one before, so I think we should go prepared for anything. Thank you Lt."

Elizabeth took a deep breath and prepared to call in John's team to bring him home.

oOo

Nick followed behind Ronon and the marines as they led the way into the building. They had brought three jumpers with marines, medical personnel, and several of the Baradians, not trusting the message saying Sheppard and the others were being released. The smell of disinfectant met him as they slid silently down the long hall. Lorne motioned for him to stay where he was as they entered the room at the end of the corridor. Only two life signs had been detected in the building, but they were taking no chances.

Nick glanced into the room the marines had checked earlier to see a metal table surrounded by equipment and trays of instruments. He winced at the sight of restraints and straps attached to the table, silently hoping none of that had been used on Sheppard and the others.

Lorne's grim face looked around the corner at him. "Doc, you better get in here."

Nick swallowed hard and shuddered at the Major's expression and tone of voice as he carried his bag through the doorway. Two beds were occupied, one by Sheppard and the far bed by one of the Baradians. He quickly moved to the Colonel and let the Baradian healers tend to their man. Kelly was ushered in behind him and he could hear one of the marines reporting to Lorne just behind him.

"Building is clean, sir. Looks like they cleared out just like they said."

Nick relaxed a little as he took in Sheppard's condition. His patient was pale and sweaty, his eyes closed. Two bags similar to IV bags hung from poles and attached to each arm. He examined the bandages around the arm, opening it up to see where the catheter entered the vein. Noting the way the line looked, he was surprised they had kept the bandages on, assuming maybe they were being extra protective about infection. He wished he knew what was in the bags. Another bandage covered Sheppard's stomach and two ports exited the central area of the bandage. He carefully examined the entrance point and was happy to see no sign of infection. Whoever had done this to the Colonel had at least used sterile procedures and kept the wounds clean. He lifted the sheet to see the Colonel also had a catheter. Pushing the sheet back just enough to examine it, he found no sign of trauma or infection there either. He quickly restored the sheet to cover his patient.

Kelly had already released John from the wrist and ankle restraints on her side of the bed. Nick hurriedly freed John's other wrist and ankle and then looked up to see if she had taken vital signs yet.

Kelly was just pulling the blood pressure cuff off Sheppard's arm. "His pulse is 60 and weak, his pressure is 90/64 and his temp is 100.5." Nick took out his stethoscope and listened to Sheppard breathe. He'd noted the oxygen mask and was concerned about the need for it. He could hear a rattle in the Colonel's lungs, his breaths heavy and wheezing.

Nick turned to Lorne. "Didn't someone say whoever took them was leaving a record of what they had done?"

"I think this is it." Nick turned to see Rodney picking up a disc and flashing it so he could see. He walked up to stand beside Nick, Ronon and Teyla accompanying him. "How is he?"

"Hard to tell until we get him back to Atlantis. At least he's alive."

John moaned, pulling all their attention to him. His head rolled on the pillow and then his eyes fluttered open. He blinked a few times and then seemed to focus on Nick. He flinched when Kelly took his hand, but she held on and began to stroke the back of his wrist and hand. She frowned at the red ring around the man's wrist where he had struggled against the restraints at some point. The fact that the marks were faint indicated he'd been too weak or too drugged to fight very hard. She listened as Nick began to speak softly to the Colonel.

"Hey, Colonel. I know you're probably in some pain right now, but we're going to get you back to Atlantis where we can get you sorted out, okay buddy? I just need you to hang on for me."

John swallowed and looked from Nick to his teammates standing beside and behind him. "Are you real?" he whispered, so low they barely heard him.

Rodney flinched, but then quickly recovered. "Of course we're real. You didn't think we'd leave you here did you?"

John looked up at them, his lower lip trembling. "I wanna go home . . . please . . . take me . . . home." Tears streaked down his face, his voice barely audible through the mask.

Kelly frowned and swallowed hard as she wiped his face with her hand. She'd never seen him shed tears before and she knew something bad had happened to cause them now. Teyla stepped up beside Nick and leaned her head down to touch John's. "We will take you home, John. We promise."

John's eyes slid closed and his body went limp. Teyla jerked up, looking at Nick in fear. Nick checked John's pulse and then gave her a nod and a small smile. "We'd better get him back to Atlantis. Dr. McKay, be sure to bring that disc."

Rodney nodded. "Don't worry, it won't leave my sight." He looked from Sheppard to Teran. "What were they doing and where are the other two?"

"The other two men are dead. Their bodies were in a makeshift cold room, kind of like a morgue. The Baradians are taking the bodies back to their home planet," said Lorne.

Nick shook his head. "I have no idea what they were doing. Maybe the disc they left us will explain, or maybe Colonel Sheppard can tell us. We need to get him back to the infirmary as soon as possible." After he had unhooked the alien monitoring equipment, he motioned to two of the marines to bring the litter over so they could transfer Sheppard. Nick kept watch over his patient while the soldiers moved him from the bed to the litter. Once he was settled, they began carrying the Colonel back to the jumper. It was going to be a long night.

oOo

Elizabeth shivered as Rodney finished recounting what had happened on the planet. Beckett had taken the disc to see if held information that could help treat Sheppard. She could only imagine how horrible the last two weeks had been for John, being strapped to a bed and experimented on, apparently operated on as well. She watched the doorway they had taken John through, willing it to open. Not knowing what he'd been exposed to, Nick and Carson had taken him directly to isolation to examine him.

She jerked when the door opened and jumped to her feet, her heart rate increasing as they rushed forward to meet Carson and his grim expression.

Carson motioned them all back to the chairs they had just vacated and took one himself. Pausing dramatically, he scrubbed his head. "I'm not even sure where to start. We've scanned the files you brought us and run several tests. It appears they surgically modified the Colonel's stomach to hold an embryo for a brief period of development. Rodney can check the disc out while we're in surgery and fill you in on the hows and whys."

"They were using him as an incubator?" asked Rodney incredulously.

Carson nodded. "In a manner of speaking, yes. They've been pumping him full of fluids to dilute the toxins released by the embryo and drugs that were needed for the young one to develop properly. His liver and kidneys have almost shut down, which is the reason for the swelling, if you noticed it. They also suppressed the immune system so it wouldn't attack the embryo, and he's developing a bit of infection, in spite of the precautions they took. If they hadn't been so tedious about sterility, he'd be dead by now."

"You said you're going to do surgery. Can you fix him back like he was?" asked Ronon.

"Aye, I think we can. They knew what they were doing. The incisions were clean and sutured well, or whatever they did to close him up was done well. It's a matter of undoing their modifications, removing the shunts they've added, and closing the openings. Nick is already scrubbing and I'm letting him lead because of his experience putting injured soldiers and their digestive systems back together. The embryo is dead, so we have to get it out of him quickly before we have more problems to deal with. It will take a while to settle the chemical imbalances and get his immune system on line again. He's also developed some bedsores from his continued restraint in one position, although they aren't nearly as bad as I would have expected. Nick indicated there seemed to be some sort of special padding under the areas prone to such injuries. I haven't even touched on the emotional trauma of all this and that will play a big role in his recovery."

"But he'll be all right?" asked Rodney.

Carson hesitated. "He's fighting an infection with a compromised immune system, Rodney. We've taken cultures to try and identify the best antibiotics to use, but that will take some time. He's extremely weak and I'm not sure if we're dealing with liver and kidney damage yet or to what extent. It's too early to say. We'll do everything we can for him. Now, I need to get scrubbed. We'll be in there a while, so you may want to catch a bite to eat or a cup of coffee while you're waiting."

"Thank you, Carson," said Elizabeth as they stood. She watched as Carson went back through the doors and then looked at the others. "Coffee anyone?"

Teyla took a deep breath and looked up at Elizabeth. "I could use a cup of tea."

Elizabeth nodded. "We might as well entertain ourselves for a few minutes in the mess hall. Maybe it will make the time go faster."

Rodney nodded. "Let me check with the nurse for that disc. Maybe we can find out why they did this to Sheppard and the others."

"Does it matter why?" asked Ronon.

Rodney shrugged his shoulders. "No, it doesn't change how wrong it was, but I'm just kind of curious how a race cold justify something like this to themselves. I'll meet you in the mess hall in a few minutes." He watched as they nodded and left and then went to find the nurse.

oOo

Carson pulled off his gloves and dumped them in the proper container as Sheppard was wheeled out of surgery.

"You want to talk to them or you want me to?" asked Nick, disposing of his own set of gloves.

"I will," said Carson. "You did a good job, Nick."

Nick sighed and looked at his boss. "Thanks. It should never have needed to be done at all. He's going to have a hard time with this one. Getting him back on food after a trauma is always a battle and it's going to be tougher this time. I just can't imagine what must have gone through his mind the last two weeks." An involuntary shudder raced down his spine.

"Aye, but he's a tough one and we'll be here to help him. I'd better go see his team before there's a mutiny."

Nick nodded. "I think I'll go sit with him for a while, unless you need something else."

"No. I'm sure I'll be bringing you some company shortly. They'll want to see for themselves that he's still in one piece."

"Can't blame them for that," Nick said softly as he left the room.

Nick was triple checking the monitor and IV lines when Carson led Sheppard's team to his bed. He could see each of them studying the still form of the Colonel or checking out the monitors and lines running to and from the pilot. An oxygen mask covered most the Sheppard's face, and with new bandages covering the fresh incisions on his stomach, he didn't look very different than when they had rescued him several hours earlier.

"Can we sit with him?" asked Rodney.

Carson looked at Nick, who flashed him a brief smile, and then back at Rodney. "One at a time. We can't have the area around the bed cluttered in case of a crisis and we'll be monitoring him pretty closely. But considering what happened to him, it might not be a bad idea to have one of you here in case he wakens. He's liable to be disoriented and confused and you could probably calm him faster than anyone."

Rodney nodded. "Okay, me first."

They quickly set up a schedule of Colonel sitting for the next twenty-four hours and then the rest of the team shuffled out. Carson stood beside Rodney, watching Nick fuss almost nervously with Sheppard's lines.

"You could almost feel sorry for them if they hadn't done this to him," said Rodney softly.

"Aye. They were just trying to get their species to survive. If only they had just asked for help."

"Well, if they could do something like this, then maybe they don't need saving. How could you justify experimenting on someone like this?"

Carson looked at Rodney sadly. "You mean like we did to Michael?"

Rodney sputtered for a moment, trying to get his words in order. "No . . . that's not the same thing. Michael was a Wraith, not a human. This is not the same thing at all."

Carson sighed. "Isn't it? We experimented on another life form to further our own chances of survival. How is that different from what they did? They weren't even trying to save their own lives, but trying to save their species from dying out."

Rodney crossed his arms defiantly. "Well, at least we weren't trying to eat them."

Carson shook his head and looked at Nick, who shrugged his shoulders. "He does have a point."

Rodney smiled smugly. "See, he agrees. He said I have a point."

"Actually, you both have valid points."

Rodney's smile turned into a scowl. "You must have been hanging around Elizabeth. Too diplomatic."

"Just food for thought, Rodney. Let me know if the Colonel stirs." Carson gave a final nod and started for his office to look over Sheppard's test results some more.

"Carson," Rodney said softly, catching the doctor by the arm. "Don't . . . don't say anything to Sheppard about this, you know, about comparing what they did to him to what we did to Michael. He was on board with that and he doesn't need anything else to deal with right now."

Carson nodded. "I'm not a bloody fool, ya know. I would never even bring that up in front of the lad. But I'm glad to see that you realize it."

Rodney let the comment go and settled in to watch Sheppard sleep while Carson slipped out behind him. Nick sat down in a chair on the other side. "Hope you don't mind if I stick around a little while, Dr. McKay. I'd just like to make sure he's settled."

"No, I think he'd like that actually."

oOo

John could hear movements around him and he fought to finish waking up. He could feel the mask on his face and he could smell the antiseptic in the air. His eyelids fluttered open enough he saw a flash of white as he felt something grab his arm. Utter and complete panic filled him as he jerked away with a cry. Realizing his arms were no longer restrained and feeling more hands touching him, he rolled as hard as he could to his left, trying to get away from the creatures.

John impacted something soft, but solid and felt it give way. And then he was falling for a brief instant before hitting the cold, hard floor with an oomph. He landed on his stomach and yelped at the sudden stabbing pain. Hands were grabbing him and pulling him, causing him to kick and flail his arms in panic.

"No . . . no more . . . please, no more . . . please . . . just kill me. You're going . . . to have to kill me . . . just . . . no more . . . " His voice trailed off to a pitiful cry and a whimper as his energy played out and he could no longer struggle. There were at least two bodies on the floor with him, pinning him down, and another hovering over him. Soft hands touched his face and there were voices. Why were there voices? The creatures never spoke, except in his head.

"Colonel . . . John, please . . . we are trying to help you. You are home, in Atlantis. We will not hurt you."

John finally got his eyes open to find his head cradled in Kelly's lap while she gently stoked his head. Ronon was on the floor beside him, his arm across John's chest. He released his grip now that John was no longer fighting them and sat up. Nick was kneeling beside him and leaned back from where he'd been helping pin his patient down. Carson was standing behind Nick and looked like he'd been about to get in the foray.

"I'm . . . home?" John asked weakly.

Nick and Carson's faces relaxed, now that John had settled down and realized where he was. "Yes, you're home in Atlantis," said Nick with a small smile.

John let out a deep breath. "Sorry . . . thought I was . . . " His voice trailed off and he grimaced, closing his eyes. "Sorry," he whispered.

Nick placed a hand on John's shoulder. "No, it's okay. You had every right to react the way you did. We should have been more careful."

John's face burned with humiliation. He'd panicked, totally freaked out in front of one of his team and a room full of people. So how much trust would that garner him as military commander of Atlantis.

"Sheppard, any one of us would have reacted like that. You have nothing to be ashamed of," said Ronon. "After years on the run, I've been known to wake up and lash out in confusion, especially when injured. Anyone who faults you for that has never been there."

John gave a tiny nod, grateful for what the former runner was trying to say, even if he didn't wholeheartedly believe it.

"John, we need to get you off this floor," said Nick, concern in his voice. "You're bleeding and you've ripped all your lines loose."

John lifted his head a bit to see blood smeared on the floor, himself, and the people he had grappled with. Monitor pads and an IV tube dangled freely, while his oxygen mask lay on the disheveled bed.

Carson worked to put the bed in order and then stood back. "Ronon, could you give us a hand?"

Ronon and Nick got on either side of John to lift him to his feet and then into the bed. They did all the work since the Colonel was too weak to do much beyond hold his head up. After replacing the oxygen mask, Nick removed the bloody, hanging dressing from John's stomach and made a clicking noise. "He's pulled some of the stitches. We'd probably better do a scan to make sure he hasn't torn any internal ones."

Carson nodded. "I'll get it set up. Kelly, could you start another IV?"

Kelly nodded as she cleaned and bandaged the back of John's left hand. "We'll go to the other side."

John looked down at the white gauze wrapped around his forearms. "They gave me two IVs," he said in a monotone. "The clear stuff wasn't bad, but the blue stuff hurt." He looked up to find her watching him, a slight frown creasing her forehead. "I'm sorry I freaked out. I just . . . I saw the white and I thought I was back there. I'd rather die than go back there."

Kelly's frown deepened and her eyes grew moist. "You never have to go back there. Not ever. I'm sorry we scared you. I don't want you to worry about any of this. We're going to get everything taken care of. This was our fault, not yours. Now just relax and we'll get you fixed up."

John didn't say anything. He lay limply as Kelly and Nick worked to clean him up and get all the lines and wires back in place. When Nick pulled the privacy curtain and asked Kelly to get a new catheter, he felt the panic begin to rise again. Nick almost immediately noticed the rise in his heart rate.

"Colonel, are you okay? Am I hurting you?"

John fought to control his voice. "No . . . no catheter."

Nick frowned, looking down at him. "Colonel . . . you aren't really in any shape to be getting up and we've got you on some pretty strong medicine. You may be out of it for extended periods. I think the catheter will make things easier on you."

"Please," he whispered from under the mask. "They just . . . please."

Nick sighed and finally nodded. "All right, but you'll have to use a bedpan for a day or two at least. And we may have to wake you periodically."

John's relaxed his clenched jaw and took a deep breath. "Okay."

Nick pulled the curtain back to find Carson waiting. "We're ready to do the scan."

Nick nodded. "Good, I think he's ready." He decided to wait for a private moment to relay Sheppard's request to Carson.

By the time they finished the scan, Elizabeth and the rest of the team were back in the infirmary, summoned by Ronon after John's tumble from the bed. They milled around until Carson and Nick finally finished their evaluation and Carson came over to see them.

"I'm guessing Ronon told you what happened," said Carson. When the group nodded, the doctor continued. "Well, the good news is that he didn't tear anything internally. The bad news is that Nick is having to put about half of the external stitches back in. Other than that and a few bumps, he doesn't seem any worse for wear."

"How is his fever?" asked Teyla.

"It's starting to creep up a bit. He's running around 100, sometimes 101. The Tylenol seems to be handling it all right for now. I'm hoping for more information about a proper antibiotic later today. His lungs are a little more congested, but his liver and kidney functions are picking up a bit. If we can keep this infection from taking hold, I'll feel much better about his recovery."

"Can we see him?" asked Elizabeth.

Carson nodded. "Aye, I think Nick has him settled again. Maybe seeing his team will make him feel better." Carson led them to Sheppard's bed, where he was talking to Nick.

Teyla immediately put her hand on his shoulder, smiling down at John and his drooping eyelids. "You look tired, Colonel. I hope you are feeling better."

John looked up at her. "I'm good," he rasped from under the oxygen mask. His eyes swept over his friends, standing around his bed. He was so relieved to be home. He'd questioned Nick about the surgery and was calmed by the fact that the embryo that had been implanted had been removed. A small part of him wanted to feel sorry for the white aliens, but after what they had done to him and the others, he just couldn't stop the anger from building when he thought about them. Part of him wanted them to die out, and that disturbed him.

"Colonel, do you need anything?" asked Carson.

John flinched at the sudden noise breaking the silence. He shook his head. He was home. What more could he need?

Carson nodded at Nick and the two doctors left the team alone with John after admonishing them not to stay long.

Rodney shifted uncomfortably, as if he found it hard to look at John. "I'm sorry we didn't get there sooner. They left the planet . . . and we couldn't track them. We tried looking for trace elements and ions, but –"

"Rodney . . . it's okay. I know." John wanted to elaborate, to tell Rodney that he knew they would never give up on him, but he just didn't have the energy or the breath.

Rodney gaped open mouthed for a moment and then gave a small, sheepish nod. "I'm glad you're back, you know, just so we don't end up with Caldwell or someone worse."

John smiled under the mask. "Thanks guys." He let his eyes close and sleep overtake him, comforted by the presence of his team and the fact that he had made it home.

oOo

"Colonel Sheppard?"

John stirred at the sound of the soft voice, calling his name. He blinked, trying to get his eyes open and functioning. "Hmmm?" he moaned, seeing a brief flash of something green just before a hand took his wrist. He flinched, but managed to avoid panicking completely. The familiar voice and the lack of white had kept him grounded, reminding him that he was home. He rubbed his eyes to finish clearing the sleep from them. Amy smiled down at him as she checked his IV. She was wearing green scrubs.

"Hey, Colonel. Just checking all your wires and tubes, and then I need to check your bandage."

John gave a small nod as he looked around the infirmary, flashing a small smile at Teyla as she stood watch over him. No one was wearing white. Nurses and patients alike wore colored scrubs, some in colors he hadn't seen before. Nick and Carson came out of Carson's office, walking toward John's bed. Carson wore a blue labcoat and Nick wore a pink one.

Chuckling, John pushed the oxygen mask off his face. "Nice coat, Nick."

Nick grimaced as he pushed the mask back down in place. "Leave that mask on, Colonel. It's there for a reason. As for the coat, you can blame the fact that I work with a bunch of women . . . and Carson."

Carson snapped his head around. "And how do you come about this being my fault?"

"Because you said you were not wearing pink under any circumstances and you're the CMO. That left me."

Amy grinned at the two men. "I happen to like it."

"You would," the two doctors replied.

"I also think it is a nice color," added Teyla with a smug smile. Amy had filled her in on the fact that pink was often viewed as a color worn by girls and women. Teyla thought making colors gender specific was backwards and narrow-minded.

Amy widened her smile before looking back down at John. "Kelly thought we should avoid wearing white since your captors were so white. She said you mentioned seeing a flash of white and thinking you were back on that horrible planet. Anyway, she decided we should add some color around here and Dr. Beckett agreed. Getting colored scrubs was pretty easy since we have a variety of colors stashed away here and there, but the doctor's coats were all white. So we dyed them each one and a few of the white scrubs as well. Personally, I think the place looks much brighter."

John listened to the sound of the oxygen hissing in the mask as he looked at her. "You did this for me?"

Amy patted him on the arm. "Of course," she said, as if the answer was obvious. "Colonel, you put your life on the line for everyone in Atlantis almost daily. This is small by comparison. Besides, I haven't heard any complaints yet. Present company excepted."

Nick grunted. "Maybe you could fix Colonel Sheppard some pink scrubs."

John glanced forlornly down at the hospital gown. "If it will get me out of this gown." As much as he hated the hospital gowns, at least he wasn't naked any more. He shuddered, remembering how vulnerable and helpless it had made him feel.

"Colonel, you okay?" asked Nick.

"Yeah," he said into the mask, trying to convince himself of that. Looking past the two doctors, he saw Elizabeth enter the infirmary. Carson seemed to realize he was watching someone and turned around.

"I'll be right back," Carson said as he left to meet Elizabeth. John watched as Elizabeth spoke to him for several minutes, making the doctor frown and shake his head. Something was wrong. He could feel his heart rate escalating. Lifting his head a little, he tried to tell what they were talking about.

"Colonel, you need to lay back and relax," said Nick, who was now right beside the head of the bed, gently pushing John back down to the mattress. John could hear his heart racing through the rapid beeps of the monitor, but he lay his head back against the pillow.

"What's wrong? Something's wrong," John wheezed.

"I don't know, let's just give them a minute." Nick continued to keep a firm grip on John's shoulder and Amy brushed a lock of stray hair from his forehead. He watched nervously as Carson and Elizabeth finally begin walking toward him.

Amy moved away from the bed, nodding at the doctors as she left and Elizabeth stepped in to take her place. "Hi, John. How are you feeling?"

John gave a short nod. "Better. What's wrong?"

Elizabeth blanched and took in a deep breath. She slipped her hand in his and squeezed. "John, I have some bad news. Teran died a little while ago. I'm so sorry."

John clenched his jaw and tightened his grip on Elizabeth's hand. For a moment, he was too breathless to speak. "What . . . happened?"

Elizabeth held his hand firmly and placed her other hand on top. "Infection. He was just too weak to fight it off."

Carson sighed. "We offered to let him come here for treatment, but the Baradians thought they could handle it."

John closed his eyes and turned his head away. He'd liked Teran and his wife. He remembered Teran telling him about having two sons. The real pain came from the fact that he'd lived through the horrors of what the aliens had done to them for two weeks and even made it home, only to die. It wasn't fair. Nothing about this was fair.

"John, talk to me."

John forced his eyes open to look at Elizabeth. He breathed shallowly, trying to shove the rushing emotions back, to gain control once again. He'd failed yet another set of people that had depended on him.

"John, please, don't shut us out. Talk to me. I know you're upset. Let us help you."

"Why?" he whispered roughly. "Why did I live and the rest of them die?"

Carson looked up at Nick and then back down to Sheppard. "I can't answer that. You were in good physical shape when you were taken. Maybe you were stronger than the others. Maybe the change in blood chemistry didn't affect you as dramatically as the others. Maybe your body handled the toxins better. There's no way to know, Colonel. Part of it may just be luck."

John snorted. "Luck. Yeah." He felt like yelling and hitting something, but he was far too weak. He couldn't even seem to breathe properly. He felt like a house was sitting on his chest. The tears that kept trying to surface were the worst. Since when had he been reduced to an emotional basket case? "Should have been me," he muttered. "Teran has a family."

Elizabeth bit her lower lip in an effort to rein in her emotions. "You have a family too, John. And we're right here. I'm sorry that Teran died, but I'm not sorry that you lived. That's just the way it worked out and you'll have to accept it."

John swallowed hard and gave a tight nod. "Can you tell them . . . how sorry I am. There just wasn't anything . . . I could do. We tried . . . but we couldn't get away."

Nick gave a small squeeze to John's shoulder. "Colonel . . . John, this was not your fault. It's not always possible to rescue yourself, although you've pulled that off more often than most. Sometimes things are beyond our control, and this was one of those times. Everyone understands that, except maybe you. You have to let it go."

John looked at him for a moment before answering. "Easier said . . . than done."

Nick smiled down at him. "I know, especially with you. Just think about it, okay."

"Kay," he said softly. "Just need . . . some time." He closed his eyes and turned his head.

Elizabeth gave his hand one more squeeze. "We'll let you get some rest now. Call me if you want to talk." She looked up at Carson and Nick and then walked away from the bed.

"Call if you need anything. We'll be close by." Nick patted John's shoulder and then he and Carson joined Elizabeth in Carson's office.

"He's really shaken up," said Elizabeth. "I guess they went through a lot together."

"Survivor's guilt," said Nick.

Elizabeth and Carson both nodded. "One more thing to deal with," said Carson. "Just what he needs at this point."

"Is he going to be all right, physically?" asked Elizabeth. "I know you said he was fighting some kind of infection as well and that their immune system had been weakened."

Carson nodded. "Aye, he is. We think we've identified the class of bacteria, though and we've started him on a more specific antibiotic. I'm hopeful it will start to clear up soon."

Elizabeth nodded in relief. "Maybe it's about time to start working on his psychological recovery as well."

oOo

John was back on the table, strapped down and unable to move. This time no drugs were making his body numb and he could feel the tube in his throat. Two of the white aliens appeared in his field of view. One of them picked up a scalpel from a tray beside him and held it over John's stomach. He watched in horror as the knife blade descended until he could no longer see it. But he felt it as it sliced through the skin and muscle of his abdomen.

"No! Stop, please!" He began to fight against the restraints as hard as he could. But they weren't restraints, they were hands. Hands were holding him down and there were voices. There shouldn't be voices. Soothing, familiar voices. Distracted, he slowed his struggles.

" . . . Rodney and you're in Atlantis. You're home, not on that nightmare of a planet. Please calm down before you hurt yourself." The voice was strained and full of fear.

"I think he's okay now, Dr. McKay."

John opened his eyes to find Rodney leaning across him, pinning his shoulders and chest to the bed. Kelly was on the other side with her hands wrapped around the IV tube taped to his hand.

"You can get off me now," John managed to whisper. He felt like someone had punched him in the gut and he winced as Rodney's weight shifted. Kelly set his hand back down beside him and adjusted the nasal cannula back in place.

"Right, sorry. We just didn't want you doing another impression of a flying fish. Nick's getting tired of stitching you up."

John rubbed the side of his face as the two people studied him closely. "Sorry . . . nightmare."

"Want to talk about it?" asked Rodney.

"No."

"Are you sure you're all right now, Colonel?" asked Kelly.

John looked at her, his expression unreadable. "Fine. I'm fine."

Kelly frowned at him and fussed with the covers for a few moments. "I'll just let Dr. Beckett know you're awake."

Rodney stood looking at him, shifting his weight and fiddling with his hands. "You want me to sit the bed up some?" he asked, looking relieved that he'd finally thought of something to say.

"Yeah, that'd be good." John shifted a bit as the head of the bed came up, trying to get comfortable. He scratched at his upper lip where the cannula were. "I hate these things."

"It's gotta be better than that oxygen mask, though. Those things are miserable."

John rubbed his throat, his eyes distant. "Not as bad as having a tube shoved down your throat," he said softly.

Rodney stood in awkward silence, staring at the floor for a while before snapping his head up. "Kelly said your temperature is down. Not normal yet, but getting close. And obviously your breathing is better. Carson thinks you'll be okay in a few weeks, you know, after you've had a chance to finish healing."

John didn't say anything, just sat staring at his feet as the uncomfortable silence returned. Rodney almost sighed in relief when Carson came across the infirmary with a mug and set it on the tray table.

"I think you're ready to try some broth, Colonel. I had it thinned, so it may not taste like much, but I want you start with something simple. Just take it slowly and drink however much you're comfortable with." Carson adjusted the height of the table and rolled it over where it sat over John's lap.

John looked at the broth and images of the gray slime popped into this head. He could see the goop sliding down the tube and disappearing under the dressing on his stomach. He remembered vividly the cramps that followed, bringing his legs up slightly against the phantom pains.

"Colonel?"

John's attention was jerked back to the present and the thought of eating anything made his stomach almost cramp with nausea. He turned his head and leaned it back into the pillow. "I can't . . . I just can't do this yet." He clamped his mouth shut against the gag he felt coming, squeezing his eyes shut and concentrating on not vomiting. He was well aware of the pain it would cause.

"It's all right, Colonel, I've taken it away."

John slowly relaxed and opened his eyes to discover the table had been moved and the cup was gone. Rodney was staring him, his face pale and his eyes wide. Carson, however, didn't look so surprised.

"It's all right, Colonel, we can try again later." Carson gave him a small, comforting smile that said he wasn't disappointed with the pilot. "We can ease you back into this, son. I know it's hard after almost three weeks without eating."

John nodded. "Thanks. It's just . . . they gave us this gray stuff . . . and it made me sick . . . It made us . . . " He trailed off as his face flushed with shame when he remembered the way the aliens had to clean him up after a bout of the cramps. He'd felt disgusting and gross and he felt that way now. John flinched when Carson gripped his arm.

"John . . . I understand. I know what they did and how humiliating it must have been. But you aren't there any more and we won't do that to you."

"I know, it's just . . . I can't make it go away. Every time I close my eyes . . . " He chuckled bitterly. "I don't even have to close my eyes. Sometimes it's like I never left and I just dream that I'm here, that I'm safe." John pounded his fist on the bed beside him. "Why can't I move past this? I've been tortured before, I've lost people before. Why can't I just let it go and move on?" Anger, frustration, and fear all came through in his voice.

Carson looked at him for a second and then took a deep breath. "Maybe you should consider talking to Kate."

John looked down at his trembling hands. "Maybe I should."

Carson relaxed, his shoulders slumping slightly. "I'll see if she can come by later today."

John nodded. "Thanks," he said quietly.

oOo

Rodney grabbed a cup of coffee and a piece of cake and joined Ronon, Teyla, and Elizabeth at a table in the mess hall.

"Rodney, are you not supposed to be with John?" asked Teyla, concern clouding her face.

"Carson kicked me out. Kate came by to talk to Sheppard and, get this, he agreed. He's doing it willingly."

Elizabeth took in a long breath and then let it out slowly. "I think that's a good sign, Rodney."

Rodney shook his head. "Sheppard practically admitted he needed help. How could that be a good sign? He never does that. He just bottles everything up and sticks it in the back closet of his mind and goes on. Everyone knows that. This is just plain scary."

"This is different," said Ronon in a voice that was soft and quiet for him. He poked absently at a nick in the table. "They didn't just torture him and he wasn't protecting anyone. It's amazing what you can take when you know you're doing it for a reason or to protect someone. You have a choice. You choose not to give up your friends or your city. There was never any choice in this."

"And he didn't even know what they were doing to him until the end," said Elizabeth. "I think the uncertainty of being tied down while alien beings did painful things to you with no chance to know what's going to happen next would terrify me more than anything."

"Did you know they operated on him while he was awake?" asked Rodney.

"What?" gasped Elizabeth.

"I read the file more completely while I was sitting with the Colonel. They gave him some sort of drug that paralyzes and numbs the whole body. He couldn't even breathe on his own because it shut down the diaphragm. They intubated him and did that surgery while he was strapped down and awake. The records say he couldn't feel it, but still . . . to know they were cutting you open . . . " Rodney paled and pushed the cake away, shuddering.

Ronon tightened his lips in an angry scowl. "I wish they had stayed around until we got there." He rolled his shoulders, as if trying to relieve an ache he couldn't reach. His team diverted their eyes, knowing he was reliving the Wraith cutting him open to plant the tracking device.

"Carson tried to get him to drink some broth, but he couldn't. I thought for a moment he was going to puke, although I'm not sure there could be anything there to throw up. I don't think I've ever seen him so . . . lost." Rodney looked up, his eyes roving around and contacting each of them. "What if he doesn't get over this?"

"He will, it'll just take time," said Ronon firmly.

"And we will do what we can to help," added Teyla.

Rodney sighed and pulled his coffee closer, staring down into the dark liquid. "I just hope that's enough."

oOo

John watched as Carson walked across the room with another mug of broth. "Colonel, I thought we might try again." He set the cup down on the tray table.

John made a face and swallowed. "I'm not sure I can do this."

"The trick is not to think about the planet and what they did to you. Make yourself focus on something else. Distract yourself."

John frowned, his stomach already starting to turn and flashes of gray mush already appearing in his mind. "How?"

"Well, how about with some company?"

John blinked, confusion written in his expression. "Company?"

Carson smiled and nodded, turning to the door of the infirmary just as Ronon, Teyla, Rodney, and Elizabeth came through, each carrying a tray of food. "You have dinner guests."

John watched in fascination as the group rambled around, noisily pulling up chairs and bumping one another, sloshing some of their drink onto the floor. He waited on Carson to yell at them, but the doctor just grinned. Looking around, he realized there were only two other patients and they had minor injuries, which explained Carson's willingness to tolerate the volume level.

As everyone found a seat, the noise level dropped. The next thing he knew, Nick came in carrying two trays, handing one to Carson as his eyes scanned the surroundings. "So, did they leave us a chair or do we get to stand?"

"We're over here." Carson carried his tray over to place it on a rolling tray table and sat on the edge of the adjacent bed. He reached out and pulled the table up so that he didn't have to balance his food in his lap like the others.

Nick grinned and nodded. "I like the way you think." Snagging another table, he mimicked Carson's motions.

Rodney leaned back in his chair and stabbed his fork in the air. "Hey, that's not fair. We don't get a table."

Carson smiled smugly. "That's really not my problem, now is it?"

John grinned and shook his head, only partially listening as Rodney continued to ramble about doctors being a selfish lot and from there wandered into his belief about why medicine was not a true science. After a few minutes, John took a sip of the broth, focusing on the presence of his friends and their voices. He was a long way from being okay and he knew it, but he felt like maybe he'd just taken a small step in the right direction.

THE END


End file.
